paper-rlsim/tools.mk at master · sbotond/paper-rlsim · GitHub

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# Paths:
BASE	=$(shell pwd)
BIN	=$(BASE)/scripts
LABELS	=$(BASE)/Info/dataset_labels.tab

# Utility targets:
.PHONY: com push

com:
	git commit -a

# Runnables:
RLSIM=$(BASE)/simulators/rlsim/rlsim
EFFEST=$(BASE)/simulators/rlsim/tools/effest
SIMNGS=$(BASE)/simulators/simNGS/bin/simNGS
COV_CMP=$(BASE)/simulators/rlsim/tools/cov_cmp
PB_PLOT=$(BASE)/simulators/rlsim/tools/pb_plot
PLOT_RLSIM=$(BASE)/simulators/rlsim/tools/plot_rlsim_report
VER_LOG  = $(BASE)/Info/soft_versions.log

# simNGS runfile:
RUNFILE_DIR=$(BASE)/simulators/simNGS/data
RUNFILE=$(RUNFILE_DIR)/s_3_4x.runfile

# Build tools:

$(SIMNGS):
	@echo Building simNGS.
	@cd $(BASE)/simulators/simNGS/src; make
$(RLSIM):
	@echo Building rlsim.
	@cd $(BASE)/simulators/rlsim; make
$(EFFEST):
	@cd $(BASE)/simulators/rlsim/tools; make
tools: $(RLSIM) $(SIMNGS) $(EFFEST) ver

ver:
	@echo BWA `bwa 2>&1| grep Version` > $(VER_LOG)
	@echo samtools `samtools 2>&1| grep Version` >> $(VER_LOG)
	@$(BIN)/py_versions >> $(VER_LOG)
	@( source load_ensembl; $(BIN)/ensembl_versions >> $(VER_LOG))

GLOB_REP_DIR=$(BASE)/reports
GLOB_REP	=$(GLOB_REP_DIR)/global_bias_report.pdf
DIR=

gr:
	@echo Generating global report.
	@$(BIN)/plot_global_report -l $(LABELS) -c `find $(BASE)/Bias -name "meta_cov_cmp.pk"` \
	-p `find $(BASE)/Bias -name meta_pb_sim*.pk` -r $(GLOB_REP) -bc $(BASE)/Replicate/*/log/cov_cmp.pk \
	-bp $(BASE)/Replicate/*/log/meta_pb.pk